6ISK | pdb_00006isk

SnoaL-like cyclase XimE

PDB DOI: https://doi.org/10.2210/pdb6ISK/pdb

Classification: LYASE
Organism(s): Streptomyces xiamenensis 318
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-11-16 Released: 2019-11-20
Deposition Author(s): He, B., Zhou, T., Bu, X., Weng, J., Xu, J., Lin, S., Zheng, J., Zhao, Y., Xu, M.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.242 (Depositor), 0.252 (DCC)
R-Value Work:
0.210 (Depositor), 0.222 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Enzymatic Pyran Formation Involved in Xiamenmycin Biosynthesis

He, B., Zhou, T., Bu, X., Weng, J., Xu, J., Lin, S., Zheng, J., Zhao, Y., Xu, M.

(2019) ACS Catal 9: 5391-5399

DOI: https://doi.org/10.1021/acscatal.9b01034

Macromolecule Content

Total Structure Weight: 34.78 kDa
Atom Count: 1,935
Modeled Residue Count: 240
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XimE, SnoaL-like domain protein	A, B	158	Streptomyces xiamenensis 318	Mutation(s): 0 Gene Names: ximE EC: 4.2.99
UniProt
Find proteins for U5Q2N8 (Streptomyces xiamenensis) Explore U5Q2N8 Go to UniProtKB: U5Q2N8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	U5Q2N8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLA (Subject of Investigation/LOI) Query on MLA Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], F [auth B]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.242 (Depositor), 0.252 (DCC)
R-Value Work: 0.210 (Depositor), 0.222 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.894	α = 90
b = 79.894	β = 90
c = 111.721	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-11-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81473105

Revision History (Full details and data files)

Version 1.0: 2019-11-20
Type: Initial release
Version 1.1: 2020-06-03
Changes: Database references
Version 1.2: 2024-03-27
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.